Is there a way to control the Alpha of the Freestyle lines by Sun Direction?
You can fake it with the Distance from Object modifier.
The distance from specified object will then control the transparency.

How to:
1) In your Freestyle Line Style go to the Alpha tab and add the Distance from Object modifier.
2) Set the Blend mode to Subtract
3) Set your Target object. (from which the distance will be measured)
4) Set Min/Max Range for best result. (or use the Fill range by selection button)
5) Done.

Line Style setings


Result